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Ko Wen-je grew up in a modest household. His father had aspirations for Ko, as the eldest son, to become a medical doctor. After graduating from National Hsinchu Senior High School, he was accepted into the Medical School at NTU.[4][5]

Upon graduation, Ko placed first nationwide on the medical qualification exams and received his medical license. On the advice of his professor, Dr. Chu Shu-hsun, Ko decided to specialize in surgery and critical care within the department of Emergency Medicine, working on the front lines of the emergency room. After working in emergency services for 11 years, Ko traveled to the United States in 1993 for a one year clinical fellowship program on artificial liver research at the University of Minnesota under Wei-Shou Hu.

After returning to Taiwan in 1994, Ko continued to work in the emergency room while at the same time beginning his Ph.D. studies at NTU. With an invitation from Dr. Chu Shu-hsun, Ko helped found NTU's first organ transplant team with the goal of doing heart transplants. With the hope of increasing the transplant success rate, Ko brought in ECMO treatment from the US, and improved transplant success rate from 19% to 51%. On 30 January 2008, Ko set the world record for keeping a patient alive with ECMO machine for 117 consecutive days.[6] Using the US treatment standards as a guide, Ko established a set of standards for organ transplant procedures in Taiwan that was later promulgated throughout Taiwan by the then Department of Health.

In 2002, Ko received his PhD degree in clinical medicine from NTU. Aside from his work improving medical technology in Taiwan, Ko has since the year 2000 participated in many foreign medical conferences in the People's Republic of China (PRC), where he was also responsible for introducing ECMO treatment to the nation.

On 15 July 2006, Ko wrote an article for the Min Sheng Daily titled "Reflections, Errors, and Apologies: Chao Chien-ming" that received considerable media attention and led to a number of politics-related interviews. On 18 November, Ko used ECMO to save the life of Shao Hsiao-ling, wife of Taichung MayorJason Hu, who had fallen into a coma after a car accident.[7][8] This incident in particular and the media attention it drew caused Ko Wen-je to become a household name.

In 2010, Ko introduced the American concept of Integrated Care to Taiwan, and established the Integrated Care Unit at NTU Hospital with the aim of reducing treatment cost and improving quality of treatment and quality of life for the attendant doctors and nurses. Ko directed the emergency care team that treated Sean Lien (Lien Sheng-wun) for critical wounds after he was shot in the face through-and through at close range with a 9mm pistol on 26 November. Lien recovered quickly which led the media to speculate on the veracity of his story, but Ko quickly came forward to verify his claims.[9]

On 24 August 2011, Ko was held responsible for an organ transplant error and subsequently reprimanded by the university hospital (NTUH) and the Ministry of Health in Taiwan. He was the acting director for a standard organ transplant procedure which organs were taken from a coma patient who was also HIV-positive to 5 awaiting patients. In 2012, the Control Yuan accused Ko of misconduct for violating organ transplant procedure.

In May 2013, the Investigation Bureau of the Ministry of Justice suspected Ko of involvement in the misappropriation of National Science Council funds by creating fraudulent receipts, and asked Ko for an itemized list of payment details. Ko was thus drawn into the Accounting Act Amendment scandal, but the Control Yuan never brought charges. In June that year, Ko's emergency trauma care student Dr.Tseng Yue-tsee was hit by a drunk driver and sustained major trauma. She was brought to the Far Eastern Memorial Hospital.[10] Ko went to the hospital as soon as he was notified and overseeing her treatment, but was unable to save her life at the end. As a result of this incident, Ko started a foundation for the prevention of drunk driving. In August, Ko was invited by Control Yuan councilor Huang Huang-hsiung to attend a conference in Beijing and to visit Yan'an, Shaanxi Province. Ko became more focused on politics and announced his candidacy for Taipei City Mayor on 6 January 2014.

Ko provided support from the medical community when Chen Shui-bian was elected as Taipei City Mayor in 1994,[12] as well as during his 2000 Presidential bid where he ultimately took off two weeks of work to support Chen's fundraising efforts.[13] Ko is also a long-time member of the “Friends of A-bian Club”. As President, Chen opened the Ketagalan Institute in 2003, but the school was suspended for 3 years starting in 2008 after Chen stepped down and corruption charges were brought against the former President. In November 2012, the school resumed enrollment and Ko enrolled in a month-long course as a student under the guidance of Legislator Gao Jyh-peng, a long-time friend of Chen's.[14][15][16]

On 20 June 2012, Ko organised a small treatment team for Chen Shui-bian whose condition had worsened since his imprisonment, and issued a public statement signed by many prominent individuals in the medical community to demand Chen be released for medical treatment.[17] Ko has made numerous statements expressing his view that Chen should be released for treatment, and has also expressed his view that Chen's prosecution was purely political.[18][19][20][21][22][23]

Ko has mentioned that his strategic goals are the same as those of the DPP.[26] He has expressed his dislike for the KMT on numerous occasions.[27] However, in September 2016, he reiterated that he would not join DPP and remain independent until his mayoral term ends.[28]

On the evening of 6 January 2014, Ko announced his candidacy for Taipei City Mayor. On 16 January, he set up his campaign office and began bringing in campaign staff and volunteers.[29][30][31] During a symposium in Kaohsiung, Ko revealed that the accusations of misconduct in the AIDS transplant incident were the main cause of his decision to run for Mayor.[32] After announcing his candidacy, Ko was hesitant about whether or not he should join the DPP and run as the DPP candidate.[33][34][35][36][36][37][38] He ultimately decided to run as an independent, but retain coordination with the DPP.

During the DPP primaries, Ko refused to debate DPP candidates Annette Lu and Wellington Koo on numerous occasions.[39][40][41][42] A number of "slips of the tongue" made it into the news, for example when Ko said that the "Lawyer Culture" of Taiwan should end, when he criticised Koo Lee-hsiung's Facebook posts grieving over the death of Trong Chai as "too emotional," and when he possibly unintentionally revealed confidential patient information.[43][44][45][46][47][48][49][50][51][52][53]

After Pasuya Yao made it through the first round of DPP primaries, Ko agreed to a debate on 12 June and subsequently won the DPP polls.[54][55] On 16 June, the DPP agreed not to put forward a candidate for the election, and to support Ko as representative of the Pan-Green Coalition without forcing Ko to join a party.

On 10 November, Ko announced his intention to reject further monetary donations to his campaign, as the amount received by 31 October exceeded the NT$87 million cap set for Taipei mayoral elections.[56]

In October 2014, reports surfaced that according to Ethan Gutmann, an investigative writer who testified before the U.S. Congress on forced organ harvesting, Ko reportedly visited China in 2004 and tried to negotiate good prices for the organs illegally harvested from newly executed Falun Gong practitioners.[58] Ko denied the accusation, and said he told Gutmann that there were some doctors in Taiwan who had been involved in buying or selling organs for transplant, but that he was not one of them. He added that he did not know whether the organs came from Falun Gong practitioners or not, and that he only stated in the interview with Gutmann that the majority of organ sources in mainland China were unclear.[59] Ko's office stated that a recording of a conversation between Gutmann and Ko drastically contradict with details provided by Gutmann. Ko has also designated an attorney to request Gutmann to correct all false allegations in his book. Gutmann responded saying he had not said that Ko was involved in the organ trade and that he might have been intentionally misinterpreted.[60][61]

On 27 November, Ethan Gutmann released a legal response with lawyer Clive Ansley, stating that "no English speaking reviewer of the book has understood page 255 in the way it has apparently been understood in Taiwan by readers whose first language is Chinese", meaning that he has never accused Dr. Ko of being an organ broker. Instead, the readers have praised Ko for his significant contribution to "the international effort to expose the medical crimes which continue to be perpetrated in China." In addition, Gutmann and Ansley state that "the book was peer-reviewed by three expert readers and subjected to a lengthy internal editing process by Prometheus. This review included not only the text itself, but also the author's notes, interview tapes, and electronic communications."[62] In the endnotes of The Slaughter, Gutmann says he gave Ko an advance draft of the section, and that Ko signed off on it, and only a few minor edits were made afterwards.[63] A full explanation, including the actual email correspondence where Ko signed off on the story for publication, was provided by Gutmann in December.[64]

Ko's wife, Chen Pei-chi, was born in Penghu, Taiwan.[73] She graduated from Makung Senior High School and NTU's Department of Medicine. She is the director of Pediatrics for Taipei City Hospital, Heping Women and Children's Centre. Ko and Chen had an arranged marriage, and have three children: one boy and two girls.[74] It has been known throughout Taiwan that as a mayor Ko currently earns less than his wife. He once joked that in order to pay off their housing mortgage, his wife still could not retire early.[75]